[Bioperl-l] GI to taxonomy

[Paul Cantalupo]

Hello all,

It works for me if you just change 'source' to '-source'.

Paul

Paul Cantalupo
University of Pittsburgh


On Mon, Sep 16, 2013 at 10:58 AM, Bernd W <bernd.web at gmail.com> wrote:

> Hi Chris, Brian,
>
> Indeed, according to NCBI docs
> (http://www.ncbi.nlm.nih.gov/books/NBK25500/), the base URL should be:
>
> http://eutils.ncbi.nlm.nih.gov/entrez/eutils/
>
>
> Example seach:
>
> http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=science[journal]+AND+breast+cancer+AND+2008[pdat]
>
>
> Kind regards,
> Bernd
>
> On Mon, Sep 16, 2013 at 4:39 PM, Fields, Christopher J
> <cjfields at illinois.edu> wrote:
> > That's possible; there are various eutils interfaces scattered
> throughout bioperl, so it's possible some haven't been updated to the most
> recent URL.  Brian, does a modified URL work?
> >
> > chris
> >
> > On Sep 16, 2013, at 8:08 AM, Brian Osborne <bosborne11 at verizon.net>
> wrote:
> >
> >> Chris,
> >>
> >> Bio::DB::Taxonomy::entrez uses this URL by default:
> >>
> >> http://www.ncbi.nih.gov/entrez/eutils/
> >>
> >> Should it be using this one?
> >>
> >> http://eutils.ncbi.nlm.nih.gov/entrez/eutils/
> >>
> >> Brian O.
> >>
> >> On Sep 13, 2013, at 4:06 AM, Alexey Morozov <
> alexeymorozov1991 at gmail.com> wrote:
> >>
> >>> Dear colleagues,
> >>> I have a bunch of fasta genomes annotated only by their GI numbers, and
> >>> need to get a taxonomy for all of them. So I rewrote get_tree method
> from
> >>> Bio::DB::Taxonomy:
> >>>
> >>> 12 open GIS, GI_FILE;
> >>> 13 my $tax_db=Bio::DB::Taxonomy->new(source=>'entrez');
> >>> 14 my $tree;
> >>> 15 while (<GIS>)
> >>> 16         {
> >>> 17         print "Requesting data for GI $_\n";
> >>> 18         my $taxon=$tax_db->get_taxon(-gi=>"$_",-db=>'nucleotide');
> >>> 19         if ($@){die $@;}#Catch exception and die, just in case
> >>> 20                 # or die "Cannot get taxonomy data for GI$_:$!\n";
> >>> 21         if ($tree)
> >>> 22                 {
> >>> 23                 $tree->merge_lineage($taxon);
> >>> 24                 }else
> >>> 25                 {
> >>> 26                 $tree=Bio::Tree::Tree->new(-node=>$taxon);
> >>> 27                 }
> >>> 28         }
> >>>
> >>> This (line 18) way to invoke Bio::DB::Taxonomy->get_taxon is
> documented and
> >>> I expect to get taxon objects. Yet all I get is
> >>>
> >>>
> >>> --------------------- WARNING ---------------------
> >>> MSG: Must have provided a valid HASHref for -params
> >>> ---------------------------------------------------
> >>> Requesting data for GI 15604717
> >>>
> >>>
> >>> ------------- EXCEPTION: Bio::Root::Exception -------------
> >>> MSG: Can't query website: 400 URL must be absolute
> >>> STACK: Error::throw
> >>> STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:472
> >>> STACK: Bio::DB::Taxonomy::entrez::get_taxon
> >>> /usr/share/perl5/Bio/DB/Taxonomy/entrez.pm:247
> >>> STACK: ./get_tax:18
> >>> -----------------------------------------------------------
> >>>
> >>> Directly using Bio::DB::Taxonomy::entrez doesn't help, GI numbers load
> OK,
> >>> so I have no clue what happened.
> >>> Need help.
> >>> --
> >>> Alexey Morozov,
> >>> LIN SB RAS, bioinformatics group.
> >>> Irkutsk, Russia.
> >>> _______________________________________________
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> >>> Bioperl-l at lists.open-bio.org
> >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>
> >>
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